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The Pinkie Conundrum
- When Pinkie and The Doctor start playing a game of questions, the first question she asks him is "Why are you so sad?". It just goes to show how much she cares about everypony she meets.
- Celestia telling Twilight that she's better than she thinks she is and that she won't perform a FaceHeel Turn like her future self from Traveler.
- When The Doctor enters his memory room he looks upon all his old friends with fondness. Doubles as a Tear Jerker since it's entirely possible he'll never see them again.
- When The Doctor gets fed up with all of Pinkie's personal questions he asks her why she cares so much. Her answer?Pinkie: Because I'm your friend.
- The Doctor notices the TARDIS has a lot more bedrooms and kitchens than she ever had before and starts to wonder why. He eventually realizes that the TARDIS reformatted herself to encourage The Doctor to keep the Mane 6 around.
Game of Stones
- The Doctor immediately coming to Sweetie's aid after she breaks Rarity's clock.
- Applejack immediately declaring they have to help find The Lost
- Leonard's Dad had the opportunity to deny the fact he had a child with an Earth Pony, which would save his social status. He didn't.
- Oreo refusing to abandon AJ, despite the fact that she seems completely insane to him, and he just met her a few hours prior.
- AJ and Dash wonder what to do about Marr's rampage. They try to figure out What The Doctor Would Do. Rainbow lampshades that he would try to Talk Her To Death. AJ points out that it's not a bad idea, and they do a beautiful job.
- Later, The Doctor does the same thing.
- Marr finding out that she isn't The Last of Her Kind.
- We find out that Leonard used Twilight as the model for the pony equivalent of the Mona Lisa.
- The bittersweet romance between Leonard and Twilight, once Twilight reins in her fangirling over being in the presence of a scientific and cultural icon. They only get one night together, but it's one night between two ponies who have extraordinary respect and admiration for each other and as mentioned above, Twilight continues to be Leonard's muse long after she and the Doctor have to leave.
Along Came A Spider
- All of Mane characters, not just the Mane 6, absolutely refuse to let Zecora die.
- Any of the visits to Zecora while she's sick.
- The young Zecora considers her father to be a coward, so it's Heartwarming in Hindsight to hear her praise him in the present day.
- The Doctor is quick to go to life-saving mode when he sees the sick boy in spite of the fact that he really didn't want to go on the trip to Zebrica in the first place.
- Fluttershy comforts a young Zecora, even though she has no reason to.
- In return, the young Zecora defends Fluttershy from the Ash-Stripe soldiers, and later saves her life.
- The Doctor stops joking around when he sees Twilight captured.
- The CMC getting back together.
- The Doctor points out that Twilight is still incredibly helpful and intelligent even without her magic.
- A sort of Meta-Heartwarming moment is that the Anasi is actually one of the spiders from Planet of the Spiders rather than one of the Racnoss. Most fanfic writers have a tendency to focus entirely on the New Series and draw little from the Classic Series, so it's nice to see that that isn't the case here.
- The Doctor leaving Zecora a letter of apology.Doctor: Its not everyday one sends a bouquet of poisonous ferns to try and make amends, but I suppose there is a first time for everything. I do not know how long you were standing there, and Im sorry if what you heard that day scared you, but while I cannot honestly deny all of Anasis words, I promise that what she had to say was not the whole truth. If you ever want to talk about what happened or if you ever need help: Press the button. If not, then I can promise that you will never see me again. I cannot express in words how truly deeply sorry I am that events came to pass as they did. I never wanted to frighten you. Until next we meet, should you deem it to be so, The Doctor.
- Somewhat of a Tear Jerker, though, as it's implied that Zecora is still too terrified of The Doctor to take him up on his offer.
- The Reveal that Fluttershy's bravery led to Zebrica turning into a beautiful, fertile land.
A Hearth's Warming Tale
- It's a Christmas Episode. This fic is full of them.
- Pretty much anything involving the next generation of Cutie Mark Crusaders. Dawn, Cream, and Daring, whom are all but outright stated to be Twilight, Pinkie, and Rainbow's daughters. Sort of Fridge Heartwarming is that their families are still friends after all these years, especially since it is established they've met the old crusaders.
- The Doctor treats the situation like Anyone Can Die, much to Scootaloo's shock. The Doctor explains he always thinks like this because it keeps him working at his best.
- Scootaloo explaining to Gus how they're Not So Different.
- The Doctor, despite it not being the same holiday, is absolutely serious about making sure he saves the day in time for Hearth's Warming. He doesn't. Scootaloo does.
- Gus finally taking his level in kindness.The Doctor: Halfway out of the dark.
- Gus getting over eleven years of depression.
- Scootaloo's Dad makes it home in time.
- Thanks to The Doctor's help.
- And he got Scootaloo a cloud bed, just like she wanted.
- The Doctor and Gus join Scootaloo for a Hearth's Warming Dinner.
- At the beginning, Luna explains she can only tell this story once. Because she promised Scootaloo.